add back in the option to disable water entropy calculations

Author: harryswift01

CodeEntropy/config/arg_config_manager.py

@@ -59,6 +59,11 @@
         "default": "output_file.json",
     },
     "force_partitioning": {"type": float, "help": "Force partitioning", "default": 0.5},
+    "disable_water_entropy": {
+        "type": bool,
+        "help": "If set to True, disables the calculation of water entropy",
+        "default": False,
+    },
 }
 
 

CodeEntropy/entropy.py

@@ -43,7 +43,8 @@ def execute(self):
         start, end, step = self._get_trajectory_bounds()
         number_frames = self._get_number_frames(start, end, step)
 
-        if self._universe.select_atoms("water").n_atoms > 0:
+        has_water = self._universe.select_atoms("water").n_atoms > 0
+        if has_water and not self._args.disable_water_entropy:
             self._calculate_water_entropy(self._universe, start, end, step)
 
             if self._args.selection_string != "all":

config.yaml

@@ -2,13 +2,14 @@
 
 run1:
   top_traj_file:
-  selection_string: 
+  selection_string:
   start:
-  end: 
+  end:
   step:
   bin_width:
   temperature:
   verbose:
-  thread: 
-  output_file: 
+  thread:
+  output_file:
   force_partitioning:
+  disable_water_entropy: